Inferring gene expression dynamics from reporter protein levels.
We present a mathematical method for inferring the dynamics of gene expression from time series of reporter protein assays and cell populations. We show that estimating temporal expression dynamics from direct visual inspection of reporter protein data is unreliable when the half-life of the protein is comparable to the time scale of the expression dynamics. Our method is simple and general because it is designed only to reconstruct the pattern of protein synthesis, without assuming any specific regulatory mechanisms. It can be applied to a wide range of cell types, patterns of expression, and reporter systems, and is implemented in publicly available spreadsheets. We show that our method is robust to a several possible types of error, and argue that uncertainty about the decay kinetics of reporter proteins is the limiting factor in reconstructing the temporal pattern of gene expression dynamics from reporter protein assays. With improved estimates of reporter protein decay rates, our approach could allow for detailed reconstruction of gene expression dynamics from commonly used reporter protein systems.
Brown
David
D
Department of Mathematics and Computer Science, Colorado College, Colorado Springs, CO 80903, USA. dbrown@coloradocollege.edu
Lostroh
C Phoebe
CP
D000465:Algorithms; D019677:Artificial Gene Fusion; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D017930:Genes, Reporter; D049452:Green Fluorescent Proteins / Q000378:metabolism; D008957:Models, Genetic; D011401:Promoter Regions, Genetic; D011993:Recombinant Fusion Proteins / Q000378:metabolism*; D012808:Sigma Factor / Q000235:genetics / Q000378:metabolism; D001616:beta-Galactosidase / Q000378:metabolism
D001426:Bacterial Proteins; D011993:Recombinant Fusion Proteins; D012808:Sigma Factor; C069567:sigma factor KatF protein, Bacteria; D049452:Green Fluorescent Proteins; D001616:beta-Galactosidase